I went round in circles for a few hrs trying to get this working. The problem was that the advice I could find was either incomplete or pertained to FreeBSD 8.x or below. It seems methods have changed a bit for ipv6 under FreeBSD 9.x

Here's what I did after creating the tunnel at HE:

edit rc.conf with the following. Substitute your nic for re0.

ipv6_network_interfaces="re0"
ifconfig_re0_ipv6="inet6 accept_rtadv"
ip6addrctl_policy="ipv6_prefer"

...then reboot, then as root run the usual commands you'd use to get gif0 up.